Export Group BigWigs — getGroupBW • ArchR

This function will group, summarize and export a bigwig for each group in an ArchRProject.

getGroupBW(
  ArchRProj = NULL,
  groupBy = "Sample",
  normMethod = "ReadsInTSS",
  tileSize = 100,
  maxCells = 1000,
  ceiling = 4,
  verbose = TRUE,
  threads = getArchRThreads(),
  logFile = createLogFile("getGroupBW")
)

Arguments

ArchRProj: An ArchRProject object.
groupBy: A string that indicates how cells should be grouped. This string corresponds to one of the standard or user-supplied cellColData metadata columns (for example, "Clusters"). Cells with the same value annotated in this metadata column will be grouped together and the average signal will be plotted.
normMethod: The name of the column in cellColData by which normalization should be performed. The recommended and default value is "ReadsInTSS" which simultaneously normalizes tracks based on sequencing depth and sample data quality. Accepted values are "None", "ReadsInTSS", "nCells", "ReadsInPromoter", or "nFrags".
tileSize: The numeric width of the tile/bin in basepairs for plotting ATAC-seq signal tracks. All insertions in a single bin will be summed.
maxCells: Maximum number of cells used for each bigwig.
ceiling: Maximum contribution of accessibility per cell in each tile.
verbose: A boolean specifying to print messages during computation.
threads: An integer specifying the number of threads for parallel.
logFile: The path to a file to be used for logging ArchR output.

Examples


# Get Test ArchR Project
proj <- getTestProject()

# Get Group BW
bw <- getGroupBW(proj, groupBy = "Clusters")